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- PDB-1vmd: Crystal structure of Methylglyoxal synthase (TM1185) from Thermot... -

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Basic information

Entry
Database: PDB / ID: 1vmd
TitleCrystal structure of Methylglyoxal synthase (TM1185) from Thermotoga maritima at 2.06 A resolution
ComponentsMethylglyoxal synthase
KeywordsLYASE / TM1185 / METHYLGLYOXAL SYNTHASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / cytosol
Similarity search - Function
Methylglyoxal synthase / Methylglyoxal synthase, active site / Methylglyoxal synthase active site. / Methylglyoxal synthase-like domain / MGS-like domain profile. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain / Rossmann fold ...Methylglyoxal synthase / Methylglyoxal synthase, active site / Methylglyoxal synthase active site. / Methylglyoxal synthase-like domain / MGS-like domain profile. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Methylglyoxal synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Methylglyoxal synthase (TM1185) from Thermotoga maritima at 2.06 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methylglyoxal synthase
B: Methylglyoxal synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4306
Polymers41,1672
Non-polymers2634
Water2,558142
1
A: Methylglyoxal synthase
B: Methylglyoxal synthase
hetero molecules

A: Methylglyoxal synthase
B: Methylglyoxal synthase
hetero molecules

A: Methylglyoxal synthase
B: Methylglyoxal synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,29118
Polymers123,5026
Non-polymers78912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area23770 Å2
ΔGint-317 kcal/mol
Surface area33310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)130.243, 130.243, 130.243
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 5 / Auth seq-ID: 5 - 160 / Label seq-ID: 17 - 172

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Methylglyoxal synthase / / MGS


Mass: 20583.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: mgsA,TM1185 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0R7, methylglyoxal synthase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.5
Details: 15.0% Ethanol, 0.2M Li2SO4, 0.1M Citrate pH 5.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Jan 7, 2004
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→91.89 Å / Num. obs: 22616 / % possible obs: 98.4 % / Redundancy: 5 % / Biso Wilson estimate: 44.63 Å2 / Rsym value: 0.111 / Net I/σ(I): 9.2
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 2 % / Mean I/σ(I) obs: 0.8 / Num. unique all: 1449 / Rsym value: 0.701 / % possible all: 87.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMAC(5.2.0005)refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1b93

1b93


Resolution: 2.06→91.89 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.873 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. TWO CHLORIDE IONS WERE MODELLED ACCORDING TO DENSITY 3. TWO SULFATES ARE MODELLED IN DUE TO ITS PRESENCE IN IN CRYSTALLIZATION ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. TWO CHLORIDE IONS WERE MODELLED ACCORDING TO DENSITY 3. TWO SULFATES ARE MODELLED IN DUE TO ITS PRESENCE IN IN CRYSTALLIZATION CONDITION, THEY COULD BE PHOSPHATE.
RfactorNum. reflection% reflectionSelection details
Rfree0.21884 1163 5.2 %RANDOM
Rwork0.16732 ---
obs0.16998 21411 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.559 Å2
Refinement stepCycle: LAST / Resolution: 2.06→91.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 12 142 2642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222622
X-RAY DIFFRACTIONr_bond_other_d0.0010.022486
X-RAY DIFFRACTIONr_angle_refined_deg1.571.9763563
X-RAY DIFFRACTIONr_angle_other_deg0.88535766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1455331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89823.525122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31815485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3751523
X-RAY DIFFRACTIONr_chiral_restr0.0960.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022888
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
X-RAY DIFFRACTIONr_nbd_refined0.2130.2472
X-RAY DIFFRACTIONr_nbd_other0.1780.22289
X-RAY DIFFRACTIONr_nbtor_other0.0830.21473
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2113
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.215
X-RAY DIFFRACTIONr_mcbond_it2.29331790
X-RAY DIFFRACTIONr_mcbond_other0.6733646
X-RAY DIFFRACTIONr_mcangle_it2.92252577
X-RAY DIFFRACTIONr_scbond_it5.32381137
X-RAY DIFFRACTIONr_scangle_it7.41111974
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21211
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
903medium positional0.150.5
1407loose positional0.445
903medium thermal1.072
1407loose thermal2.5810
LS refinement shellResolution: 2.056→2.109 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 63 4.29 %
Rwork0.24 1407 -
obs--86.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.426-0.4212-0.09321.6386-0.19721.91080.09110.2175-0.1302-0.1694-0.0699-0.03450.13860.0062-0.0212-0.13980.07060.0315-0.1031-0.0327-0.192447.2926.3415.112
25.43853.1286-5.53473.1027-6.248537.02760.5597-0.67030.02130.6833-0.3753-0.0836-1.30190.6969-0.1844-0.0358-0.03740.0054-0.0581-0.0494-0.051256.73337.63537.554
31.9781-0.6415-0.17861.70390.18920.91880.03160.19290.1536-0.2115-0.0298-0.1089-0.1057-0.016-0.0018-0.12630.03490.0355-0.13750.0302-0.189543.465947.14316.8255
421.81381.9345-13.18190.2072-1.624513.7796-0.78031.5363-0.9774-0.31040.03460.05830.7419-1.25860.74570.091-0.0172-0.04140.0896-0.18560.030822.50532.3679.839
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 14017 - 152
22AA141 - 160153 - 172
33BB5 - 14017 - 152
44BB141 - 160153 - 172

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